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JTAG will always work, regardless of the setting on the MSEL pins - in a sense they are bypassed. However, for the FPGA to boot from the EPCS the MSEL pins
must be correctly set for AS mode.
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Well - there was a thread some time ago dealing with a false MSEL-Pins configuration (one of the not assigned combinations) and the Cyclone did not work on JTAG as well. Modification of the board manually resolved this, thus the failure was not due to faulty PCB or device...
I think the MSEL configuration (e.g. AS - mode) must be bypassed internally when accessing by JTAG, but I would not be sure that JTAG is working for any configuration of the MSEL Pins at all..
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